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In Bernard Malamud’s The Natural, Iris (played in the movie version by Glenn Close) tells Roy Hobbs that we all have two lives, “the life we learn with and the life we live with after that.”

Murray Gell-Mann, the Nobel laureate physicist who died Friday, May 24, at age 89, also lived two lives. But both were spent learning — about how the world works.

In his first life Gell-Mann was perhaps the preeminent theoretical physicist of his era, playing a prime role in revealing the architecture of the subatomic world. In his second life he pioneered the study of complexity, probing the behavior of systems ranging from economics to the weather, too complicated for the reductionist methods of particle physics.

Gell-Mann was sometimes a controversial character, quick to criticize and defensive when confronted with criticism. But he was universally acknowledged as an intellectual titan, a man whose mind grasped the mechanisms of nature with a clarity of insight rare even among other geniuses. As Niels Bohr said when comparing Ernest Rutherford to Galileo, Gell-Mann “left science in quite a different state from that in which he found it.”

By far, Gell-Mann is most famous for the idea of quarks, the building blocks of most Earthly matter. Before 1964, physicists believed that atoms assembled themselves from only three fundamental parts — electrons, protons and neutrons. Electrons even today remain indivisible. But Gell-Mann suspected that protons and neutrons — the constituents of the atomic nucleus — concealed smaller particles within.

In the 1950s, physicists playing around with ever more powerful atom smashers had discovered a zoo of other elementary particles. In the early 1960s Gell-Mann perceived patterns in the properties of those particles, realizing they could all be related by certain mathematical symmetries. His analysis of those patterns enabled him to predict the existence of a particle (he called it the omega-minus) not yet discovered. Subsequent experiments found his particle, with just the properties that Gell-Mann predicted.

His arrangement of the known particles in groups was reminiscent of Mendeleev’s periodic table of the elements. “I was playing around with the particles. He was playing around with the elements. It was natural to make a comparison between them, although I think Mendeleev’s work was much more important,” Gell-Mann told me when I interviewed him in 1997. It was the relationships among the known particles that led him to suppose that previously unimagined particles lived within protons and neutrons. The protons and neutron should be a part of the system, not separate fundamental particles unto themselves, he reasoned. “The idea of neutrons and protons alone being fundamental was totally absurd,” he told me.

But his first attempt to describe inner constituents dismayed him — the math required them to possess electrical charges that were fractions of the electron’s (or proton’s) charge, a seeming deal breaker. He recalled sketching out the equations on a napkin when queried on that point by fellow physicist Bob Serber. Serber seemed satisfied, but Gell-Mann reconsidered. He thought it over and decided maybe fractional charges could be allowed if the particles possessing them never appeared in experiments, remaining trapped inside the proton or neutron. So he described the quarks (named for the sounds made by gulls mentioned in James Joyce’s Finnegans Wake) as mathematical or “fictitious.” While others took that to mean the quarks were mathematical conveniences, rather than real physical particles, Gell-Mann later claimed that he used “fictitious” just to mean that they couldn’t be seen. “By fictitious or mathematical I meant that they were trapped inside — couldn’t get out,” he insisted.

Today quarks’ reality is unquestioned. And much of Gell-Mann’s other work remains relevant, embedded in the foundation of modern particle physics, called the standard model. But in the1980s, Gell-Mann switched lives, moving on from his traditional particle physicist niche at Caltech to the avant-garde approach to science practiced in New Mexico at the Santa Fe Institute, which he cofounded. There Gell-Mann and others pursued the science of complexity, a new field that yielded mixed results at first but with some significant successes (aiding the understanding of the biological complexities of the immune system, for example). At Santa Fe, Gell-Mann advocated new methods of quantifying complexity and explaining complex adaptive systems (he called them IGUSes, for information gathering and utilizing systems). He explored new approaches to understanding languages beyond traditional linguistics and worked on a new interpretation of quantum mechanics, producing a series of important papers with his collaborator James Hartle.

During his second life Gell-Mann also advocated strongly for research into superstring theory, the mathematical apparatus that seemed a promising approach to unifying quantum mechanics with Einstein’s supposedly incompatible general relativity (the theory of gravity). Gell-Mann harshly criticized physicists who claimed superstring theory was unscientific because of the impossibly high energies needed to actually detect the strings. But inability to detect strings directly does not invalidate the theory, Gell-Mann argued, because possibly other consequences of the theory could be observed. The energy needed to probe the unification of gravity and other forces is not the same as “the energy at which you can detect some phenomena that are related to the theory. It’s a really stupid mistake to mix those two things up,” he said.

While superstring theory has yet to fulfill its advocates’ hopes, Gell-Mann remained a fan. “To this day,” he said when I interviewed him last a decade ago, he believed “that possibly superstring theory has something to do with the long-sought unified theory of all the forces and all the particles.”

Gell-Mann often expressed his comments about other physicists rather bluntly. When I asked him about the difference between his quantum mechanics interpretations and the work of others that seemed similar, he replied, “the difference is that we do it right and they do it wrong.”

When I asked what he thought of one prominent physicist’s work, Gell-Mann responded, “I don’t know what he’s talking about.” As for another, a Nobel laureate: “He’s a crank.” Yet there were others whose work he praised, including Rolf Landauer (“a very clever fellow”), Andy Strominger (“very bright”) and of course Hartle, his quantum collaborator. And Gell-Mann was also often very supportive of young physicists and could be engaging and cordial, even with some (though not all) journalists.

In a wide-ranging interview in 2009, Gell-Mann expressed to me his concern with science’s frequent lack of openness to researchers challenging conventional wisdom. “Most challenges to scientific orthodoxy are wrong,” he said. “A lot of them are crank. But it happens from time to time that a challenge to scientific orthodoxy is actually right. And the people who make that challenge face a terrible situation — getting heard, getting believed, getting taken seriously.”

He called the inherent opposition of traditional science to daring novelty “the pressure of received ideas.” Escaping it was a prime reason for living his second life in Santa Fe, at the institute he helped to organize, where the pressure to conform to traditional norms was diminished. “In Santa Fe it is relatively easy to be free of that,” he said. “If we were at a great center of intellectual prestige and so on it would be much harder, much harder to be free of the pressure of received ideas.”

Of course, some of today’s received ideas deserve to withstand any future challenge. Gell-Mann’s quarks, and much of his other work, are likely to be among them.